+Open data
-Basic information
Entry | Database: PDB / ID: 1ulr | ||||||
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Title | Crystal structure of tt0497 from Thermus thermophilus HB8 | ||||||
Components | putative acylphosphatase | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Ago, H. / Hamada, K. / Sugahara, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of tt0497 from Thermus thermophilus HB8 Authors: Ago, H. / Hamada, K. / Sugahara, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ulr.cif.gz | 31.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ulr.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ulr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/1ulr ftp://data.pdbj.org/pub/pdb/validation_reports/ul/1ulr | HTTPS FTP |
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-Related structure data
Related structure data | 2acyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9694.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKS6, acylphosphatase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.47 Å3/Da / Density % sol: 15.88 % |
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Crystal grow | Method: micro batch using tera / Details: micro batch using TERA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→33.73 Å / Num. obs: 18506 / % possible obs: 63.7 % |
Reflection shell | Resolution: 1.09→1.13 Å / % possible all: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ACY Resolution: 1.3→33.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.027 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.975 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→33.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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